CVTree A Parallel Alignment-free Phylogeny and Taxonomy Tool based on Composition Vectors of Genomes

Manual

Main Programs

  • cvtree: the main program, it gets the phylogenetic tree from the fasta files of genomes.
  • g2dv: Get the composition vectors based on the fasta files of genomes.
  • cv2dm: Get the distance matrix based on the composition vectors
  • dm2tree: Get the phylogenetic tree based on the dissimilarity matrix.
  • cvdump: Show composition vector
  • mconv: convert formats of the dissimilarity matrix file
  • getdist: Show select dissimilarity from the dissimilarity matrix
  • diffmtx: compare two dissimilarity matrixes

Installation

Compile with CMake

Preparation

  • cmake >= 3.0
  • g++ >= 4.8 or other compiler supporting C++11 standard
  • require ligrary: libz
  • compiler with support openmp for parallel (option)
  • Library (option): netcdf, netcdf_cpp
  • Library (option): libhdf5 for c++ (Please don't use the hdf5 libraries in Anaconda)

Compiling

  1. unzip the package file and change into it
  2. mkdir build and change into it
  3. cmake .. or add some options you wanted
  4. make
  5. make install (option)

Run Programms in Docker

Docker allows users to run programs on both Windows and Linux/macOS. You can download docker free and reference docker document to install it. After install docker, basic usages for CVTree are:

  1. Build/download docker image: docker build -t="cvtree-img" . or docker pull ghzuo/cvtree. In this step, a image with cvtree programs will obtained. Here option "-t" set the image name. After build the image, you can delete the dangling images for build by docker image prune.
  2. Start container from the image: docker run --rm -it -v $PWD/example:/root/data cvtree-img In this step, you will enter the cvtree container, and the "example" folder of this project will be found in the "data" folder. Change path to the data folder, and run cvtree -G faa. You will get the result for eight genomes in the "list" file. You can change the path "$PWD/example" to your own data directory.
  3. Exit and stop container: exit in docker terminal.
  4. Run cvtree in docker by one command: docker run --rm -v $PWD:/data -w /data cvtree-img cvtree -G faa
  5. More usage for docker can reference docker document.

Run Programs with Example

If this is the first time you use CVTree package, please go to the "example" folder. Edit "list" to include the genome names, and run the cvtree command to get the phylogeny tree by:

../build/cvtree -G faa

More detail of the command usage can be obtained by -h option.